Hi Pavel
When you say "I can clearly demonstrate it", does "it" refer to the fact
that Rfree gets biased? Have you explored how strong the effect is?
To date, I'd laboured under the impression that real and reciprocal
space are numerically very different things, i.e. what you refer to as
"model seeing reflections", how it sees them in real space is not
equivalent to how it sees them in reciprocal space. i.e. no harm done
including them in maps.
But come to think of it, I only thought that because someone had said it
(on the BB?). So do you have something better, actual numbers?
Cheers
Frank
Hi Robbie,
On 24/04/2014 16:26, Pavel Afonine wrote:
I agree with Ed that you probably should not leave out your free
reflections in real-space under normal circumstances.
Phoebe is right: you should not use free-r reflections in calculation
of map that you are going to use for real-space refinement. Otherwise
you will be biasing Rfree: the strength of the effect depends on how
much model you will be real-space refining. I can clearly demonstrate
it with a simple cctbx based script that I can post later of anyone
interested. Ed's point about zeros is a good one, but here we are
talking about specific set of non-zero reflections (free reflections)
that we do not want to "see" any model, any refinement. If by "under
normal circumstances" you mean real-space refinement of only a tiny
fraction of the model (say a residue or a few residues) followed by
reciprocal space refinement then this may not visibly impact the
Rfree; however, still, technically this will make free-r reflections
"see" your model and some refinement, which isn't cool I think.
All the best,
Pavel
